Main
Kasia Kedzierska
I am a PhD student at the University of Oxford. As a computational biologist, I use Data Science and Machine Learning to answer biological questions. Specifically, I study cancer of the uterus and chromatin organisation in disease progression. Last summer, I joined Computational Biology Department at Novo Nordisk Research Centre in Oxford as an intern, where I was working with NLP methods and knowledge graphs.
Selected Research Experience
Intern
Novo Nordisk Research Centre Oxford
Oxford, United Kingdom
2021
- I used NLP based methods to screen biomedical artciles and identify potential therapeutic targets. I built R Shiny App to allow colleagues within the company to investigate results from our pipeline.
DPhil Candidate
Mentored by D. Church and D. Woodcock
University of Oxford, UK
present - 2018
- PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer
Visiting Graduate Student
Ratan group
University of Virginia, USA
2018 - 2017
- Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
- Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.
Research Assistant
Zebrafish Developmental Genomics
IIMCB, Warsaw, Poland
2016 - 2015
- I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics.
- I was responsible for both computational and experimental aspects of the project.
Education
DPhil. Candidate, Genomic Medicine and Statistics
Nuffield Department of Medicine, Brasenose College
University of Oxford, UK
present - 2018
- PhD fully funded by Wellcome Trust Four-year PhD Studentships in Science
M. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2018 - 2015
- Thesis: Analysis of the mutational burden across gene sets in cancer.
- Thesis awarded the best Master thesis in Bioinformatics defended in 2018 title.
Publications
Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift
M. Migdal, E. Tralle, K. A. Nahia, L. Bugajski, K. Z. Kedzierska, F. Garbicz, K. Piwocka, C. L. Winata, M. Pawlak
BMC Genomics
2021
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis
Clinical Epigenetics
2020
Prognostic integrated image-based immune and molecular profiling in early-stage Endometrial Cancer
N. Horeweg, M. de Bruyn, R. A. Nout, E. Stelloo, K. Kedzierska, A. León-Castillo, A. Plat, K. D. Mertz, M. Osse, I. M. Jürgenliemk-Schulz, L. C.H.W. Lutgens, J. J. Jobsen, E. M. van der Steen-Banasik, V. T. Smit, C. L. Creutzberg, T. Bosse, H. W. Nijman, V. H. Koelzer and D. N. Church
Cancer Immunology Research
2020
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata
Genome Research
2019
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
K. Jividen, K. Z. Kedzierska, C.-S. Yang, K. Szlachta, A. Ratan and B. M. Paschal
BMC Cancer
2018
SONiCS: PCR stutter noise correction in genome-scale microsatellites
K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler
Bioinformatics
2018
Selected Talks and Posters
Analysis of the mutational burden across gene sets in cancer
Polish Bioinformatics Society Symposium
Cracow, Poland
2019
- Invited talk
Differential mutation analysis across gene sets in cancers
The Biology of Genomes 2018
Cold Spring Harbor, NY, USA
2018
- Poster
Selected Awards and Honours
Senior Hulme Scholarship
N/A
N/A
present - 2021
- Senior Hulme Scholarship is awarded by Brasenose College, University of Oxford to DPhil students whose academic performance is deemed to be exceptional.
Best Master Thesis in Bioinformatics
N/A
N/A
2019 - 2018
- Analysis of the mutational burden across gene sets in cancer - Best Master Thesis defended in Bioinformatics in 2018 in Poland.
Attended Workshops, Summer Schools
Machine Learning Summer School
Imperial College London, University College London
London, United Kingdom
2019
Teaching Experience
Data visualization in bioinformatics - hackathon mentor
Online hackathon NGSprint
Discord
2021
- I led the hackathon in data viusalisation with emphasis on computational biology. Under my supervision, 3 teams of areound 5 people each, created interactive and captivating visualisation. Teaching materials are available at github.com/kzkedzierska/NGSprint_data_viz.
Online tutorials: Python for Data Science and Introduction to Python
YouTube
2020
- I led two Python tutorials: Introduction to Python kasia.codes/talk/intro_to_python/ and Python for Data Science kasia.codes/talk/py4ds/.
Introduction to R
Wellcome Centre for Human Genetics
Oxford, United Kingdom
2019
- 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
- Materials available on github/kzkedziersa/r_intro
Introduction to Managing Code with Git
Wellcome Centre for Human Genetics
Oxford, United Kingdom
2020 - 2019
- I led a 2-hour introduction to working with Git. Materials, including slides and exercises are available at kasia.codes/talk/into_to_git/.
Selected Grants
Visegrad Grant to organize #NGSchool2020 postponed until 2022
N/A
2022 - 2020
- 32,190 EUR awarded towards organising affordable summer school focusing on ML application in CompBio. Due to COVID-19 pandemic we organised a virtual events in 2020 & 2021 and are planning in person summer school and conference in 2022.
Non-profit Work
President
N/A
2021 - 2018
- The goal of the Society is to promote and support science, with emphasis on computational biology.
- President since 2019; Vice President 2018 - 2019